Leaving the time-travel-doesn't-HAVE-to-be-cheesy mode behind momentarily, we look at the possibility that everything we thought was wrong, the Covenant were right, and my, don't we have egg on our helmet. Er, face.

Lets assume that the Forerunners are indeed humans from whatever time period; and Master Chief is an enigma (it seems to me that the Mjolnir warriors always were). And then take into account that the Covenant stated they were "Instruments of God," or whatever. Well, what if the Covenant were symbolically right? I mean right about wanting to exterminate the humans. Its a theory that the Forerunners actually created or caused the whole Flood thing. What if the Covenant (and their little prophet-dudes) somehow know something we don't know, and are trying to prevent the humans from ever releasing the Flood? Perhaps the Covenant were right all along...

The question (or, at least one of the questions) is, "How would they know?" Whether it's a deep form of racial memory, an information altar left for later evolving generations to find, or something entirely different, however, it's not much of a stretch to imagine that the Covenant have been annihilated before, and this current galactic crusade is their attempt to ensure their own survival. It makes their fanaticism that much more... human, if you catch my drift.